MueLu: renamed RAPscripts into shell_scripts
MueLu: added python script for Hopper runs

While it is very similar to the old bash script, it is much cleaner.
Also,
* added command line parameter interpreter, which allows one to
  skip editing both arcadia.py and petra.pbs.template, so one is
  able to start new jobs with a single command line.
* added a command line option for epetra/tpetra, so that we can run
  only one of those
* base on the matrix type, the scaling is done automatically and
  correctly for both 2D (quadratically) and 3D (cubically)
* prompting user to make sure he wants to clean up
* auto table adjustment during analysis depending on whether we run
  epetra, tpetra, or both
MueLu: hopper script: minor fix
Ifpack2: SparseContainer: Simplified gather-scatter for local op.

I also added a new expert mode constructor to Tpetra::MultiVector.
I had thought it would be useful for SparseContainer.  It turned out
that I didn't need it, but it seems like it would be useful for other
reasons, so I left it in place.

Build/Test Cases Summary
Enabled Packages: Ifpack2
0) MPI_DEBUG => passed: passed=22,notpassed=0 (0.48 min)
1) SERIAL_RELEASE => passed: passed=18,notpassed=0 (0.08 min)
Kokkos: Create Kokkos::Serial device.  Enable multi-functor reduce on Kokkos::Threads device. Resolve (last?) HostMirror revisions.
Ifpack2: SparseContainer: Fixed diagonal scaling in weightedApply.

weightedApply was doing the diagonal scaling (elementWiseMultiply) with
the whole diagonal Vector D, instead of the permuted subset that it
should be using.  The "permuted subset" refers to the domain and range
of the InverseType operator.  This commit fixes that.  It makes the code
correct, and might also improve performance for small diagonal blocks.
Of course, the "small diagonal blocks" case really needs DenseContainer
for best performance, which Ifpack2 doesn't have yet.

Build/Test Cases Summary
Enabled Packages: Ifpack2
0) MPI_DEBUG => passed: passed=22,notpassed=0 (0.43 min)
1) SERIAL_RELEASE => passed: passed=18,notpassed=0 (0.05 min)
MueLu: fixing damping factor format in XML decks

There were a number of XML decks specifying the damping factor like so:

     <Parameter name="Damping factor"                      type="double" value="4./3"/>

The XML parser interprets this as a damping factor of 4!  We should expect the parser
to understand mathematical expressions, I guess.

This commit changes all such occurences to 1.333.

Thanks to Dr. PTLin for helping to locate this.
ML: minor updates to matrix reader.
MueLu: minor updates to matrix reader example
MueLu: adding a runtime information message
MueLu: improving output

Put matrix multiply and matrix add under verbosity control
Added a Statistics2 output type.
Tried to make the Low and Medium outputs reasonable:
    Low doesn't say anything about matrix stats
    Medium gives matrix stats
    Moved some details to High output
Fixed a few warnings along the way.
MueLu: updating tests that use Utils::Multiply
MueLu: adding a runtime information message
MueLu: fix conflict
MueLu: TwoMatrixAdd sig has changed.

It now takes a FancyOStream.  (So shoot me.)
MueLu: minor output change

Build/Test Cases Summary
Enabled Packages: ML, MueLu
Disabled Packages: MOOCHO
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=333,notpassed=0 (4.23 min)
1) SERIAL_RELEASE => passed: passed=310,notpassed=0 (1.84 min)
2) MPI_SS_DEBUG => passed: passed=215,notpassed=0 (14.40 min)
3) SERIAL_SS_DEBUG => passed: passed=208,notpassed=0 (11.03 min)
Other local commits for this build/test group: 0dd48b0, 814cd3b, 4e2a328, 5e6be04, 0cedfdb, 1ad4b08, e7b940f, be0ee3d, b0ac674
Add ctest coverage build file to trilinos-test2

This build is not part of the normal nightly build yet.
Tribits: Changes to support new dashboard features for coverage testing

David Cole had provided a set of changes as a start for being able to support a
coverage build that could distinguish between library and test code. This commit
applied the concepts from those commits such that the coverage build will work
without having some of the side effects that were undesirable. This required
changing what labels were attached to many of the targets that are built to
declare which part of the coverage they belong to, without breaking the
association to the package that it used to state. There was one major deviation
from the changes that David provided. The test names are not labeled with
<package_name>Test. This is because when they were labeled as such packages were
appearing on the dashboard labeled not with their name, but instead "2 labels"
since there was a <package_name> label and a <package_name>Test label for every
package with tests. This change does not affect the coverage testing because
test are cmake targets and not associated directly with source files for the
dashboard.

This also required making a few changes to the testing driver core to make sure
that the new labels were used for selecting what packages to build and to make
sure the correct set of information was submitted to the dashboard.

There is one caveat with this. To support subpackages and normal packages
cleanly normal packages end up with a redundant label for libraries. Subpackages
needed to be able to label their libraries with the subpackage's name, but to be
able to communicate to the dashboard correctly they also need to label their
libraries with the parent package's name. For Normal packages the package name
and parent package name are the same which leads to 2 identical labels being set
for normal packages. This doesn't have any visible side effects for the
dashboard, however.

For packages you will now see at least 2 labels on the coverage report.
Generally this will be "<package_name>Exes" and "<package_name>Libs" where the
Exes generally are the sources tests and Libs refers to sources compiled into a
library. For packages with subpackages there will be additional entries for each
subpackage.
Fix an issue with the trilinos-test2 nightly testing

The build type for all nightlies on trilinos-test2 was being hard coded to
release despite the fact that we had several tests trying to run debug. This
allows each test to set the correct build type.

Build/Test Cases Summary
Enabled Packages: TrilinosFramework
Enabled all Packages
0) MPI_DEBUG => passed: passed=1502,notpassed=0 (30.33 min)
1) SERIAL_RELEASE => passed: passed=1469,notpassed=0 (6.82 min)
Other local commits for this build/test group: 5734b29, ad47cab
MueLu: arcadia: analyze() can now run only for a specific petra